Exemple #1
0
        public void InitializeIsotopicIons(double ppmTolerance, double minimumPercentage = 0.05, int maxProfileLength = int.MaxValue)
        {
            var atomComposition = aas.GetPeptideAtomComposition(this.Sequence);
            var profiles        = profileBuilder.GetProfile(atomComposition, this.Charge, minimumPercentage).Take(maxProfileLength);

            this.IsotopicIons = (from peak in profiles
                                 select new IsotopicIon()
            {
                Mz = peak.Mz,
                Intensity = peak.Intensity,
            }).ToArray();
            var diff = this.TheoreticalMz - this.IsotopicIons[0].Mz;

            //Replace the ion m/z to real ion m/z but keep the distance between ions in case of the peptide contains modification
            foreach (var ion in this.IsotopicIons)
            {
                ion.Mz += diff;
                var mzdiff = PrecursorUtils.ppm2mz(ion.Mz, ppmTolerance);
                ion.MinimumMzWithinTolerance = ion.Mz - mzdiff;
                ion.MaximumMzWithinTolerance = ion.Mz + mzdiff;
            }

            this.IsotopicIntensities = (from ion in this.IsotopicIons
                                        select ion.Intensity).ToArray();
        }
    //[Test]
    public void TestWuyinPeptide()
    {
      List<String> lines = FileUtils.ReadFile(@"C:\Documents and Settings\sheng\Desktop\sequences.txt");
      var aas = new Aminoacids();

      foreach (String line in lines)
      {
        AtomComposition ac = aas.GetPeptideAtomComposition(line);
        ac.Add(new AtomComposition("H2O"));
        List<double> profile = this.ip.GetProfile(ac, 10);
        Console.WriteLine(line);
        Console.WriteLine(ac);
        foreach (double d in profile)
        {
          Console.WriteLine(d);
        }
        Console.WriteLine();
      }
    }
Exemple #3
0
        //[Test]
        public void TestWuyinPeptide()
        {
            List <String> lines = FileUtils.ReadFile(@"C:\Documents and Settings\sheng\Desktop\sequences.txt");
            var           aas   = new Aminoacids();

            foreach (String line in lines)
            {
                AtomComposition ac = aas.GetPeptideAtomComposition(line);
                ac.Add(new AtomComposition("H2O"));
                List <double> profile = this.ip.GetProfile(ac, 10);
                Console.WriteLine(line);
                Console.WriteLine(ac);
                foreach (double d in profile)
                {
                    Console.WriteLine(d);
                }
                Console.WriteLine();
            }
        }
Exemple #4
0
        public O18QuantificationPeptideProcessor(IFileFormat <O18QuantificationSummaryItem> fileFormat,
                                                 bool isPostDigestionLabelling, string rawFilename, string peptide,
                                                 double purityOfO18Water, List <O18QuanEnvelope> envelopes, double mzTolerance,
                                                 string additionalFormula, double scanPercentageStart, double scanPercentageEnd)
        {
            _fileFormat = fileFormat;
            _isPostDigestionLabelling = isPostDigestionLabelling;
            _rawFilename       = new FileInfo(rawFilename).FullName;
            _peptide           = peptide;
            _additionalFormula = additionalFormula;

            _atomComposition = _aas.GetPeptideAtomComposition(peptide);
            if (!string.IsNullOrEmpty(additionalFormula))
            {
                var additionalAtomComposition = new AtomComposition(additionalFormula);
                _atomComposition.Add(additionalAtomComposition);
            }
            _profile          = _cp.GetProfile(_atomComposition, 0, 10);
            _purityOfO18Water = purityOfO18Water;
            _envelopes        = envelopes;

            _scanPercentageStart = scanPercentageStart;
            _scanPercentageEnd   = scanPercentageEnd;
        }
Exemple #5
0
        public override IEnumerable <string> Process()
        {
            var annos      = new AnnotationFormat().ReadFromFile(boundaryFile);
            var aas        = new Aminoacids();
            var pbuilder   = new EmassProfileBuilder();
            var chroFormat = new ChromatographProfileTextWriter();

            foreach (var ann in annos)
            {
                var chroFile = Path.Combine(ann.Annotations["ChroDirectory"] as string, ann.Annotations["ChroFile"] as string) + ".tsv";
                var peptide  = (ann.Annotations["PeptideId"] as string).StringBefore("_");
                var start    = double.Parse(ann.Annotations["ChroLeft"] as string);
                var end      = double.Parse(ann.Annotations["ChroRight"] as string);

                var chro         = chroFormat.ReadFromFile(chroFile);
                var chroFiltered = chro.Profiles.Where(l => l.RetentionTime >= start && l.RetentionTime <= end).ToArray();

                //all observed isotopimers, start from 1, transfer to zero-based
                var allIsotopics = (from f in chroFiltered
                                    from s in f
                                    select s.Isotopic - 1).Distinct().OrderBy(l => l).ToArray();

                //get minimum intensity of each isotopimer
                var minIntensities = (from iso in allIsotopics
                                      select(from f in chroFiltered
                                             where f.Count > iso
                                             select f[iso].Intensity).Min()).ToArray();

                //how many isotopic should I trust?
                var iso0   = (from f in chroFiltered select f.First().Intensity).ToArray();
                int maxIso = 1;
                for (int i = 2; i < allIsotopics.Length; i++)
                {
                    var isoi = (from f in chroFiltered select f.Count > i ? f[i].Intensity : minIntensities[i]).ToArray();
                    var corr = MathNet.Numerics.Statistics.Correlation.Pearson(iso0, isoi);
                    if (corr < minPearsonCorrelation)
                    {
                        maxIso = i;
                        break;
                    }
                }
                var maxIsoArray = allIsotopics.Where(l => l <= maxIso).ToArray();

                //get observed profile in each scan
                var observedIons = (from f in chroFiltered
                                    select(from iso in maxIsoArray select f.Count > iso ? f[iso].Intensity : minIntensities[iso]).ToArray()).ToArray();

                var atomComposition = aas.GetPeptideAtomComposition(peptide);
                var hatom           = (int)(Math.Round(aas.ExchangableHAtom(peptide)));
                for (int h2 = 0; h2 < hatom; h2++)
                {
                }


                var profiles     = pbuilder.GetProfile(atomComposition, 1, 3);
                var isotopicIons = (from peak in profiles
                                    select new IsotopicIon()
                {
                    Mz = peak.Mz,
                    Intensity = peak.Intensity,
                }).ToArray();
            }

            return(null);
        }